A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.
Report
generated on 2025-03-24, 08:36 UTC
based on data in:
/mnt/lustre/RDS-live/downing/LSDV-PVG/work/0f/d291da34f7e2709261ed0dfc0edbaf
ODGI
ODGI is an optimized dynamic graph/genome implementation, for efficient analysis and manipulation of pangenome graphs structured in the variation graph model.
Detailed ODGI stats table.
| Sample Name | Length | Nodes | Edges | Paths | Components | A | C | T | G | N |
|---|---|---|---|---|---|---|---|---|---|---|
| seqwish | 32768 | 1681 | 2251 | 11 | 1 | 9774 | 7065 | 8471 | 6901 | 551 |
| smooth | 40305 | 1286 | 1722 | 11 | 1 | 12399 | 8614 | 10502 | 8682 | 108 |
Sum of path node distances
For each path we iterate from node to node and count the node / nucleotide distance of nodes on the pangenome level normalized by the path length. If a node is reversed, we count the node distance twice.
This value allows you to evaluate the sorting goodness - how linear the graph is.
Mean links length
For each path we iterate from node to node and count the node / nucleotide distance mean_links_length
of nodes within the same path only. We then normalized by the path length.
This value allows you to evaluate the sorting goodness - how linear the graph is.